GapMind for catabolism of small carbon sources

 

Alignments for a candidate for lat in Alicycliphilus denitrificans K601

Align Ornithine aminotransferase; Orn-AT; Lysine aminotransferase; Lys-AT; EC 2.6.1.13; EC 2.6.1.36 (characterized)
to candidate WP_013518270.1 ALIDE2_RS17550 aspartate aminotransferase family protein

Query= SwissProt::Q5JEW1
         (445 letters)



>NCBI__GCF_000204645.1:WP_013518270.1
          Length = 398

 Score =  202 bits (513), Expect = 2e-56
 Identities = 137/418 (32%), Positives = 217/418 (51%), Gaps = 49/418 (11%)

Query: 36  LPIVIERGEGIRVYDVDGNVFYDFASGVGVINVGHSHPRVVEAIKKQAEKFTHYSLTDFF 95
           +PI +ERG+G+RV+DV+G  + D   G+ V  +GH+HPR+V A+++Q  K  H   T  +
Sbjct: 19  VPIALERGQGVRVWDVNGKQYLDGLGGIAVNTLGHNHPRLVPALQEQIAKLIH---TSNY 75

Query: 96  YENAIILAEKLIELAPGDIER-KVVYGNSGAEANEAAMKLV-KYGTGR----KQFLAFYH 149
           Y   +   E+L  L  G        + N+G EANE A+K+  KYG  +     + + + H
Sbjct: 76  YH--VPGQEELARLLTGRARMTNAFFCNTGLEANECAIKIARKYGVDKGIEKPEIVVYDH 133

Query: 150 AFHGRTQAVLSLTASKWVQQDGFFPTMPGVTHIPYPNPYRNTWGIDGYEEPDELTNRVLD 209
           AFHGR+ A ++ T +  V+ +GF P + G   +  PN       I+  +E  E    V+ 
Sbjct: 134 AFHGRSIATMTATGNPKVR-NGFGPLLEGFIRVA-PND------IEALQEATEGNPNVV- 184

Query: 210 FIEEYVFRHVPPHEIGAIFFEPIQGEGGYVVPPKGFFKALKKFADEYGILLADDEVQMGI 269
                           A+  EPIQGEGG       + + ++K  D  G LL  DEVQ G+
Sbjct: 185 ----------------AVLMEPIQGEGGLHPMRVEYLQQVRKLCDANGWLLMLDEVQAGM 228

Query: 270 GRTGKFWAIEHFGVEPDLIQFGKAIGGGLPLAGVI-HRADITFDKPGRHATTFGGNPVAI 328
           GRTGK++A +  G+ PD++   K +G G+P+  V+ H A     KPG H +TFGGNP+A+
Sbjct: 229 GRTGKWFAHQWAGIVPDVMTLAKGLGSGVPVGAVLAHGAASEVLKPGNHGSTFGGNPLAM 288

Query: 329 AAGIEVVEIVKE--LLPHVQEVGDYLHKYLEEFKEKYEVIGDARGLGLAQAVEIVKSKET 386
            AG+E + I++E  LL +  +VG +L   L++       + + RG GL   VE+ +    
Sbjct: 289 RAGVETIRIMEEEGLLQNAADVGAHLKAGLQQALGSVPGVNEVRGQGLIIGVELDRPCGV 348

Query: 387 KEKYPELRDRIVKESAKRGLVLLGCGDNSIRFIPPLIVTKEEIDVAMEIFEEALKAAL 444
                     ++  +A+ GL+L    D  IR +P L +T+ E D  + +    ++A L
Sbjct: 349 ----------LIDRAAQAGLLLSVTADRVIRLVPALTLTRAEADEIVALLTPLVQAFL 396


Lambda     K      H
   0.320    0.141    0.418 

Gapped
Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 1
Number of Hits to DB: 493
Number of extensions: 25
Number of successful extensions: 6
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 1
Number of HSP's successfully gapped: 1
Length of query: 445
Length of database: 398
Length adjustment: 32
Effective length of query: 413
Effective length of database: 366
Effective search space:   151158
Effective search space used:   151158
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 50 (23.9 bits)

This GapMind analysis is from Apr 09 2024. The underlying query database was built on Sep 17 2021.

Links

Downloads

Related tools

About GapMind

Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.

A candidate for a step is "high confidence" if either:

where "other" refers to the best ublast hit to a sequence that is not annotated as performing this step (and is not "ignored").

Otherwise, a candidate is "medium confidence" if either:

Other blast hits with at least 50% coverage are "low confidence."

Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:

GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).

For more information, see:

If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know

by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory